bio-tools / biotoolsLint

Utility for verification of bio.tools content with reporting
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Rarer issues with PMIDs #20

Open joncison opened 5 years ago

joncison commented 5 years ago

From https://github.com/bio-tools/biotoolsRegistry/issues/281:

As reported above, sometimes there is an ID in the PMCID field that is missing the "PMC" prefix.

For two tools, the publication PMID is set as the value of the PMID field (correct) and equally also as the value of the PMCID field (incorrect): https://bio.tools/GEM_Mapper https://bio.tools/MACARON

For two other tools, the publication PMID is incorrectly set as the PMCID value only: https://bio.tools/parallelnewhybrid https://bio.tools/angsd-wrapper

For two tools, the PMCID number part is correct, just the "PMC" prefix is missing (however, in that case the PMCID resolver can still work out the correct article in PMC): https://bio.tools/GWAMA https://bio.tools/PIQMIe

These few rare errors could be avoided, if the "PMC" prefix was a mandatory part of the PMCID.

In a few rare cases a specified PMID is missing in PubMed. This doesn't seem to be a mistake made when adding an entry to bio.tools, rather the PMID was removed in PubMed itself at a later date.

This tool has the PMID "19504496", which results in a "not available" error in PubMed: https://bio.tools/sumosp

The PMIDs "24166654", "27116744" and "25504941" will result in a "was deleted because it is a duplicate of PMID" error in the following tools: https://bio.tools/BoolSpace https://bio.tools/gecko-csb https://bio.tools/ProSight_Lite

But in the last cases, the PMID resolver is able to redirect to the correct PMID (that the deleted PMID was a duplicate of). However, not all metadata sources might not be able to do this and return no results when queried with the deleted PMIDs (like https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=xml&db=pubmed&id=24166654). So it would be better to replace the deleted duplicate PMIDs with the original ones.